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Install Linux Ubuntu with spatial ecological modelling software as main OS

Preparation of an Ubuntu Linux OS

  • Download an iso linux ubuntu file from and store it on your pc
  • Open a Virtual machine player and create a new operating system from the iso file you downloaded and stored
  • Update the Ubuntu OS just created with the update manager or with the following command lines:

    sudo apt-get update sudo apt-get -y upgrade
    Install gnome3 sudo apt-get install gnome-panel
    Install gnuplot and gimp

    sudo apt-get -y install gnuplot gimp

Install some useful tools

    apt-get install tofrodos nautilus-open-terminal

Install kate editor

    apt-get install kate konsole

Install gedit

    apt-get install gedit gedit-common gedit-plugins 

In case the touchpad is not working

    sudo su 
    echo 'options psmouse proto=imps' > /etc/modprobe.d/psmouse.conf

Enrich Ubuntu 12.04 OS with gis, rs and statistical software

Add Ubuntu GIS stable repository as described in

became a super user and perform all these operations:

   sudo su     
   echo  "# Update RS and GIS SW"  >> /etc/apt/sources.list
   echo  "deb trusty main" >> /etc/apt/sources.list
   echo  "deb-src trusty main" >> /etc/apt/sources.list 
   apt-key adv --keyserver --recv-keys 314DF160 # check key number [[|here]]
   apt-get update

Install gis and remote sensing software

works on the 12 August 2013

   apt-get update
   sudo apt-get install python3-gdal python-gdal gdal-bin libgdal-dev libgdal1-dev  libgdal1h libgdal1-1.10.0-grass grass-core grass-gui qgis-plugin-grass-common qgis  python-qgis libqgis-dev   libqgis2.0.1   


 sudo su     
 echo  "# Grass7"  >> /etc/apt/sources.list
 echo  "deb precise main" >> /etc/apt/sources.list 
 echo  "deb-src precise main" >> /etc/apt/sources.list 
 apt-key adv --keyserver --recv-keys 26D57B27
 sudo apt-get update
 sudo apt-get install flex  bison libtiff4-dev mesa-common-dev libglu-dev  libfftw3-dev  libfftw3-dev libfftw3-3 libfftw3-dev  libcairo2-dev
 sudo apt-get install  python-gtk2 python-gtk2-dbg python-gtk2-dev python-wxgtk2.6 python-wxgtk2.6-dbg python-wxgtk2.8 python-wxgtk2.8-dbg
 sudo apt-get install grass70-core  grass70-gui grass70-dev grass70-dev-doc grass70-doc

grass7 add-ons

   mkdir $HOME/.grass7/addons/
   cd    $HOME/.grass7/addons
   svn co
   chmod 777 -R $HOME/.grass7/addons/raster/

in case of different $HOME/.grass7/addons/ setup grass variables GRASSADDONBASE GRASSADDONPATH (see

Install openev work whit gdal 1.2 Download the file openev-linux-180.tar.gz

 sudo apt-get libstdc++5 

on 64bit

 sudo apt-get install multiarch-support

on 64bit september 2015 try one by one and reinstall openev

 sudo apt-get install libxext6:i386
 sudo apt-get install lsb-core  
 sudo apt-get install lib32gcc-4.7-dev  

on 64bit September 2016 for 16.04

sudo apt-get install libxext6:i386
sudo mv libstdc++5_3.3.6-25ubuntu4_amd64.deb  /var/cache/apt/archives/
sudo apt-get install /var/cache/apt/archives/libstdc++5_3.3.6-25ubuntu4_amd64.deb 

Installation procedure (osgeolive 10.5 )

 sudo apt-get install libxext6:i386 lsb-core lib32gcc-4.7-dev 
 cd /tmp
 wget wget
 tar xvf openev-linux-180.tar.gz
 cd openev
 sudo ./install linux   /usr/bin/openev
 # add to the ~/.bashrc the alias openev
 echo "alias openev='/usr/bin/openev/bin/openev' "  >>  ~/.bashrc

Installation procedure Debian streach August 7th, 2017

  sudo apt-get install lib32gcc-6-dev
  sudo dpkg -i  libstdc++5_3.3.6-28_i386.deb

Installation procedure osgeolive 13

 sudo apt-get install libc6:i386
 sudo apt-get install libxext6:i386
 be sure that the link under /usr/bin/openev/lib/ are present ->

Install orfeotoolbox

deb precise main deb-src precise main

 apt-get install  monteverdi libotb3.13

 sudo apt-get install python-saga libsaga-dev libsaga

Install pktools

Enrich the OS with specific libraries

sudo apt-get install g++ gpp liblas1 liblas-dev python-liblas liblas2 liblas-c2 liblas-c-dev libboost-dev gsl-bin libgsl0-dev  libarmadillo2 libarmadillo-dev libfann-dev libfann2 libarmadillo-dev libarmadillo2


libnlopt-dev2.2.4-1~lucidamd64.deb (210.8 KiB)
libnlopt02.2.4-1~lucidamd64.deb (185.2 KiB)

Enter in the “local source” directory and allow the root rights

  cd /usr/local/src
  sudo su

Check the last version available at and download it


Untar and start the compiling action

tar xzvf pktools-2.4.tar.gz
cd pktools-2.4.tar
./configure  --enable-fann  --enable-nlopt  --enable-las  --with-gdal=/usr/bin/gdal-config
sudo make install

In some cluster you need to install pktools under your $HOME/bin by preloding some modules

 module load Tools/Python/2.7.3
 module load Libraries/GDAL/1.10.0
 module load Tools/PKTOOLS/2.4.2
 module load Libraries/OSGEO/1.10.0
 module load Libraries/GDAL/1.10.0
 module load Libraries/GSL
 module load Libraries/ARMADILLO 
 export CPPFLAGS="-I$ARMADILLO_DIR/include -I$GSL_DIR/include"
 export GSL_LIBS="-L$GSL_DIR/lib -lgsl -lgslcblas"
 ./configure --prefix=/$HOME   --with-gdal=$GDAL_DIR/bin/gdal-config 

Install R

We follow instruction as reported at

 sudo su
 echo "# added for R repository" >> /etc/apt/sources.list 
 echo "deb precise/"   >> /etc/apt/sources.list 
 gpg --keyserver --recv-key E084DAB9
 gpg -a --export E084DAB9 | sudo apt-key add -
 apt-get update 
 apt-get -y install r-base

Install R library for spatial data analysis and machine learning modelling using the CRAN Task View: Analysis of Spatial Data as suggested in

   sudo su
   install.packages(pkgs="ctv", lib= "/usr/lib/R/library",  dependencies=TRUE)
   # we selected Norway as CRAN repository

rgdal installation in the a cluster

 R CMD INSTALL   --configure-args="--with-geos-config=/usr/local/cluster/hpc/Software/BDJ/Libraries/GEOS/3.4.0/bin/geos-config --with-proj-include=/usr/local/cluster/hpc/Software/BDJ/Libraries/PROJ/4.8.0/include   --with-proj-lib=/usr/local/cluster/hpc/Software/BDJ/Libraries/PROJ/4.8.0/lib"  rgdal_0.8-16.tar.gz 

install kate and emacs tex editors

sudo apt-get -y install kate konsole emacs

install R 4 in osgeolive 13

 sudo apt update 
 sudo apt upgrade
 sudo apt-key adv --keyserver --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
 sudo add-apt-repository 'deb bionic-cran40/'
 sudo apt update 
 sudo apt install r-base r-base-core r-recommended r-base-dev

Personalize your working environment

Set your keybord type

The default keybord is the Great Britain gb english UK type

sudo echo "# USE BRITISH Keyboard"  >>    /etc/init.d/rc.local    
sudo echo "setxkbmap gb" >>  /etc/init.d/rc.local   
Modify gb with your keyboard type. Example: for USA keyboard type use “setxkbmap us”. Spanish: es; Italian: it; French: fr; German: de …. . See man setxkbmap
wiki/install_linux.txt · Last modified: 2021/01/20 20:36 (external edit)